Natural killer cells and cytotoxic T-lymphocytes are important in the immune response against virally infected cells and tumor cells. Cell mediated death occurs by two distinct mechanisms, fas/fas-ligand and granule exocytosis. One of the major components of the cytotoxic granules are serine-proteases, termed granzymes. Although the role of granzymes in causing cell death has not been established, recent experiments with granzymeB-deficient mice show it is critical for target DNA fragmentation. We have cloned rat granzyme B, C, and two other granzymes that have not yet been classified. Upon obtaining sufficient quantities of these enzymes, we would like to determine substrate subsite specificity using enzymological and structural methods. This series of homologous serine proteases presents a system for elucidating the structural determinants of substrate specificity. Additionally, a serine collagenase isolated from fiddler crab is being used to probe the interaction with its substrate, collagen. The Computer Graphics Laboratory has been used to structurally model these proteases.